Non-FRET cell based assay

ABSTRACT

Compositions and methods for analyzing protease activity, and especially BoNT/B, BoNT/G, BoNT/D, and/or BoNT/F protease activity, using a cell based assay are provided. Cells express at least two recombinant hybrid proteins each of which includes a fluorophore and a membrane anchoring peptide, and at least one of which includes a BoNT protease recognition and cleavage sequence positioned to release a fluorophore upon cleavage. Analysis is performed by monitoring fluorescence following exposure to a BoNT. The fluorophores are positioned so that no useful FRET occurs between them, permitting fluorescence produced by the non-released fluorophore to be used in data normalization.

This application is a continuation of U.S. patent application Ser. No.14/941,452, filed Nov. 13, 2015, now U.S. Pat. No. 10,246,492, which iscontinuation-in-part of U.S. patent application Ser. No. 13/502,357,filed Aug. 17, 2012, now U.S. Pat. No. 9,453,254, which claims priorityto U.S. Provisional Application No. 61/252,315, filed Oct. 16, 2009.

FIELD OF THE INVENTION

The field of the invention is cell based assays for protease activitythat utilize fluorescence but do not utilize Förster resonance energytransfer (FRET), especially protease assays for Botulinum neurotoxinsBoNTs that cleave synaptobrevin.

BACKGROUND OF THE INVENTION

Botulinum neurotoxins (BoNTs) are extremely toxic proteins and can beclassified into distinct subgroups based, inter alia, on peptidesequence and/or substrate specificity. All of the naturally occurringBoNTs (BoNT/A-G) are composed of a heavy chain that mediates toxin entryinto a target cell and a light chain with zinc-dependent proteaseactivity that hydrolyzes selected SNARE proteins that mediate fusion ofneurotransmitter vesicles to the membrane that forms part of thesynaptic cleft.

For example, the light chain of BoNT/A hydrolyzes with high specificitySNAP-25, which is required for vesicle-mediated exocytosis ofacetylcholine into the synaptic cleft. Known assays for such hydrolyticactivity include those described in our copending Internationalapplication (WO 2009/035476), which is incorporated by reference herein.Here, a fluorophore and a quencher are covalently linked to therespective ends of a peptide sequence that includes, for example, theSNAP-25 sequence. Cleavage by BoNT/A (or other BoNTs with a substratespecificity towards SNAP-25) will result in physical separation of thecleavage products and so reduce fluorescence quenching, which can thenbe quantified. Among other choices, it is often preferred that suchassay is performed as an in vitro solid-phase based assay.

While such assay is conceptually simple and can be used to readilydetermine BoNT/A, BoNT/C, or BoNT/E activity, such assay can not besimply modified to a cell-based assay for determination of BoNT/B,BoNT/D, BoNT/F, or BoNT/G activities by replacing the SNAP-25 motif witha SNARE domain as the SNARE domain includes a membrane spanningsub-domain that would place the N-terminal fluorophore into a vesiclelumen. In such case, only diffusion of the fluorescence signal would beobserved as has been reported elsewhere (Dong et al. PNAS (2004), Vol.101, No. 41, 14701-14706; or U.S. patent application Ser. No.2006/0134722).

Therefore, there is still a need for improved BoNT assays, andespecially cell-based assays for BoNTs that cleave synaptobrevin.

SUMMARY OF THE INVENTION

The present invention is directed to various compositions and methods ofanalyzing BoNT protease activity, and especially BoNT/B, BoNT/G, BoNT/D,and/or BoNT/F protease activity in a cell-based system using a pair offluorophores positioned such that no useful (e.g. less than 5%)fluorescence resonance energy transfer occurs between them. Mostpreferably, the cells express two recombinant hybrid proteins, where oneof the hybrid proteins includes at least one BoNT protease recognitionand cleavage sequence, along with a transmembrane domain that is notcleavable by the BoNT protease and that directs the hybrid protein to anintracellular synaptic vesicle.

One aspect of the inventive subject matter is a transfected cell thatproduces two hybrid proteins having a structure of A-C-B and A-C′-D,respectively, wherein A is a transmembrane domain that is not cleavableby the BoNT protease, B is a first fluorescent protein, C is a BoNTprotease recognition and cleavage sequence, C′ is a non-cleavable analogof a BoNT protease recognition and cleavage sequence, and D is a secondfluorescent protein. The first and second fluorescent proteins arepositioned such that when the two hybrid proteins are collocated on avesicle no useful FRET is produced. When such a transfected cell iscontacted with a BoNT protease it can take up the BoNT protease,resulting in release of the first fluorescent protein.

Another aspect of the inventive subject matter is a cell-based method ofmeasuring protease activity of a BoNT protease, in which in one step atransfected cell is provided that produces two hybrid proteins having astructure of A-C-B and A-C′-D, respectively, wherein A is atransmembrane domain that is not cleavable by the BoNT protease, B is afirst fluorescent protein, C is a BoNT protease recognition and cleavagesequence, C′ is a non-cleavable analog of a BoNT protease recognitionand cleavage sequence, and D is a second fluorescent protein. In anotherstep, the transfected cell is contacted with a BoNT protease underconditions to allow the cell to take up the BoNT protease, and in yetanother step, fluorescence is measured of at least one of the first andsecond fluorescent proteins in the transfected cell.

Most preferably, the transfected cell is a neuronal cell, aneuroendocrine tumor cell, a hybrid cell, or a stem cell. It is furthergenerally preferred that A includes a transmembrane domain fromsynaptobrevin, synaptophysin, synapsin I, synapsin II, and/or synapsinIII, and/or that C includes at least two of a BoNT/B, a BoNT/G, aBoNT/D, and a BoNT/F protease recognition and cleavage sequence. Whilenot limiting to the inventive subject matter, it is further preferredthat a peptide linker is disposed between one or more of A and C, A andB, C and B, and C and D, and that the linker has a length of equal orless than 12 amino acids. Additionally, it is contemplated that thetransfected cell may be contacted with a putative or known BoNTinhibitor prior to contacting the transfected cell with the BoNTprotease.

Consequently, the inventors also contemplate a cell transfected with thenucleic acid presented herein, and it is generally preferred that thecell is stably transfected with the nucleic acid. Especially suitablecells include neuronal cells, neuroendocrine tumor cells, hybrid cells,and stem cells. Furthermore, it is typically preferred that the cellcomprises a nucleic acid that encodes the two hybrid proteins having thestructure of A-C-B and A-C-D.

Various objects, features, aspects and advantages of the presentinvention will become more apparent from the following detaileddescription of preferred embodiments of the invention.

BRIEF DESCRIPTION OF THE DRAWING

Prior Art FIGS. 1A-1B are known FRET assays for BoNT protease activityin which two fluorescent proteins are separated by a SNAP25 recognitionand cleavage sequence.

FIGS. 2B-2B are schematic illustrations for intramolecular (2A) andintermolecular (2B) FRET assays for BoNT protease activity according tothe inventive subject matter.

FIGS. 3A-3B are exemplary vector maps for recombinant intramolecular(3A) and intermolecular (3B) FRET constructs according to the inventivesubject matter.

FIG. 4A depicts exemplary FRET results for intramolecular (left panel)and intermolecular (right panel) FRET analysis according to theinventive subject matter.

FIG. 4B is a graphic representation of the results from the experimentsof FIG. 4A.

FIGS. 5A and 5B schematically depict an alternative embodiment of anintermolecular assay for BoNT activity. FIG. 5A depicts the assaycomponents prior to exposure to the BoNT. FIG. 5B depicts the assaycomponents following exposure to the BoNT.

DETAILED DESCRIPTION

According to the present invention a cell-based FRET assay for BoNT (andespecially for BoNT/B, BoNT/D, BoNT/F, or BoNT/G) is provided in which acell is transfected cell such that the cell produces (a) a single hybridprotein having a structure of A-B-C-D, or (b) two distinct hybridproteins having a structure of A-C-B and A-C-D, respectively, in which Ais a transmembrane domain, B is a first fluorescent protein, C is BoNTprotease recognition and cleavage sequence, and D is a secondfluorescent protein, where most typically, B and D allow for a FRETassay.

It should be appreciated that the hybrid protein(s) that are formed inthe so transfected cells include a transmembrane domain. Therefore,these proteins are expected to locate to intracellular vesicles and toso present a vesicle-bound substrate. Upon exposure of the cells withBoNT, heavy chain-mediated endocytosis of the BoNT into the transfectedcell is followed by presentation of the light chain on the outer surfaceof the vesicle, allowing the protease activity of the light chain tocleave the cleavage sequence of the hybrid protein(s), thus reducingFRET and providing a quantifiable signal. Therefore, it should beappreciated that the compositions and methods presented herein allow fora cell-based assay in which uptake, processing, and proteolytic activitycan be monitored under conditions that closely resemble the naturalconditions.

In contrast, as schematically depicted in Prior Art FIG. 1A, a BoNT/Atest system with a hybrid protein is shown in A. The hybrid protein hasfirst and second fluorescence proteins (CFP and YFP, respectively)covalently coupled to the respective termini of an intermediate peptidesequence that also includes a SNAP-25 sequence (which is the substratefor the BoNT/A light chain protease). Excitation of the CFP results inFRET-mediated fluorescence emission of YFP, thus creating a specificspectral fluorescence signature as schematically illustrated in B. Uponincubation with BoNT/A, the SNAP-25 sequence is hydrolyzed and YFP isreleased from the hybrid molecule (the remainder of which is still boundto a membrane or other solid phase) as depicted in C. Alternatively, oradditionally, excitation and emission may be followed only using YFP,which when separated from the hybrid protein, will ultimately beprocessed in the proteasome complex. Similarly, as shown in Prior ArtFIG. 1B, a hybrid protein has first and second fluorescence proteins(CFP and YFP, respectively) covalently coupled to the respective terminiof an intermediate peptide sequence that also includes a SNAP-25sequence. The hybrid protein is associated to the outside of the vesiclevia the cysteine rich domain of the SNAP-25 sequence. Once more, uponcleavage of the SNAP-25 linker between the CFP and YFP, FRET is nolonger available and fluorescence can be measured either as loss in FRETor ultimately loss in YFP as described above.

While such systems provide various advantages, it should be readilyapparent that that where the SNAP-25 sequence is replaced by asynaptobrevin (VAMP), the presence of the transmembrane sub-domain insynaptobrevin will lead to physical separation of the CFP and YFP by thevesicle (or other) membrane, thus abolishing any FRET between the CFPand YFP as is shown in FIG. 9B of U.S. patent application Ser. No.2006/0134722.

To overcome these difficulties, the inventors now have prepared hybridmolecules suitable for intramolecular FRET in which one fluorescentprotein (or other reporter) is positioned between the transmembranesub-domain and the BoNT protease recognition and cleavage sequence, andwherein another fluorescent protein (or other reporter) is positionedfollowing the BoNT protease recognition and cleavage sequence.Additionally, the inventors have also prepared pairs of hybrid moleculessuitable for intermolecular FRET in which both hybrid molecules have arespective fluorescent protein coupled to respective sequences thatinclude a transmembrane domain and a BoNT protease recognition andcleavage sequence.

As used herein, the term “transmembrane domain” refers to any molecularmoiety that is capable of insertion into a plasma membrane in a mannersuch that at least a portion of the moiety extends into (and moretypically across) the lipid bilayer. Thus, a moiety that only externallycontacts (e.g., via ionic or electrostatic interaction) the outersurface of the plasma membrane is not considered a transmembrane domainunder the definition provided herein. Thus, especially preferredtransmembrane domains include hydrophobic polypeptide domains thatextend into (and more typically across) the plasma membrane. Mosttypically, preferred transmembrane domains comprise a (typicallyrecombinant) polypeptide. However, it should be recognized that variousalternative elements (e.g., N-terminal palmitoylation) will also fallwithin the scope of the definition provided herein.

As also used herein, the term “BoNT recognition and cleavage sequence”refers to any molecular moiety that can be bound and cleaved by a BoNTprotease. It is generally preferred that the BoNT recognition andcleavage sequence comprises a synaptobrevin polypeptide or portionthereof, which is typically a recombinant polypeptide.

In one especially preferred aspect of the inventive subject matter,contemplated recombinant nucleic acids may include a sequence thatencodes (I) a hybrid protein having a structure of A-B-C-D or (II) atleast one of two hybrid proteins having a structure of A-C-B and havinga structure of A-C-D, respectively, where A is a transmembrane domain, Bis a first fluorescent protein, C is a BoNT recognition and cleavagesequence, and D is a second fluorescent protein. Most preferably, wherethe sequence encodes two hybrid proteins, expression of the two hybridproteins is under the control of respective promoters (typically, butnot necessarily, having the same strength and same regulatory controlmechanism).

Most typically, the transmembrane domain is selected such as to allowinsertion of the recombinant protein(s) into the membrane of synapticvesicles. Therefore, it is generally preferred that the transmembranedomain is the transmembrane domain of synaptobrevin, synaptophysin,synapsin I, synapsin II, and/or synapsin III, or any portion thereofthat still confers anchoring of the recombinant protein into themembrane. However, in alternative aspects of the inventive subjectmatter, it is contemplated that various other transmembrane domains arealso deemed suitable so long as such domains will anchor the recombinantprotein to one or more intracellular membranes. There are numeroustransmembrane domains known in the art, and all of those are deemedsuitable for use herein. The person of ordinary skill in the art willreadily be able to identify a domain as a transmembrane domain (e.g.,via publication and description of the domain, or via computationaldomain analysis). Of course, suitable domains naturally occurringdomains as well as mutated forms thereof (e.g., forms with one or moretransitions, transversions, insertions, deletions, inversions, etc.).Moreover, additionally contemplated transmembrane domain may also beentirely synthetic and based on computational analysis.

Similarly, it should be appreciated that the transmembrane domain mayalso be replaced by another polypeptide moiety that allows at leasttemporary anchoring of the hybrid protein to a membrane such that theremainder of the hybrid protein is exposed to the cytosol. Anchoring maybe mediated by various (typically non-covalent) interactions, includingionic, hydrophobic, and/or electrostatic interactions. Still furthercontemplated transmembrane domains also include non-proteintransmembrane domains. For example, especially preferred alternativetransmembrane domains will include those in which a hydrophobic group(e.g., sterol, hydrocarbon, etc.) is attached to the protein, andparticularly a palmitoyl group. Such groups may be added intracellularly(e.g., via palmitoylation signal) or in vitro using various syntheticschemes.

It should further be appreciated that suitable transmembrane domainswill preferably not include a BoNT protease cleavage site and/or a BoNTprotease recognition site and thus only be acting as a transmembraneanchor for the recombinant protein. Therefore, suitable transmembranedomains may include full-length (or substantially full-length)synaptobrevin that has been sufficiently mutated to eliminate thecleavage site and/or recognition site. Alternatively, the synaptobrevin(or other transmembrane domain) may be truncated such that at least thecleavage site and/or recognition site is removed. Moreover, while theabove is directed to single transmembrane domains, it should beappreciated that more than one transmembrane domains are also deemedappropriate (which are preferably coupled to each other via a spacer).

With respect to first and second fluorescent proteins it is generallycontemplated that all known fluorescent proteins are suitable for useherein so long as such proteins can be used as specific and distinctsignal generation moieties. However, it is particularly preferred thatthe signal generation moieties are fluorescent proteins that aresuitable for FRET. For example, first and second fluorescent proteinscan be Cyan Fluorescent Protein (CFP) and Yellow Fluorescent Protein(YFP) and their respective modifications, respectively. Of course, andas already noted above, the fluorescent proteins may be modified toinclude one or more specific characteristics (e.g., spectral) or betruncated to a specific size. Among other choices, contemplatedfluorescent proteins include various blue fluorescent proteins (e.g.,EBFP, EBFP2, Azurite, mKalama1), various cyan fluorescent proteins(e.g., ECFP, Cerulean, CyPet), various green fluorescent proteins (e.g.,AcGFP1, ZsGreen1), and various yellow fluorescent protein derivatives(e.g., YFP, Citrine, Venus, YPet).

Similarly, it should be appreciated that the BoNT protease recognitionand cleavage sequence may vary considerably, so long as such sequence isstill recognized and hydrolyzed by a BoNT light chain. For example, theBoNT protease recognition and cleavage sequence may be of human, rat, ormurine origin, may be present in oligo-multimeric form, and may befurther specifically modified to facilitate or at least partiallyinhibit cleavage. Alternatively, the BoNT protease recognition andcleavage sequence may also be modified to allow identification of one ormore specific BoNT subtypes (e.g., BoNT/B, D, F, and/or G, as welltetanus toxin) by preferential or exclusive cleavage. Of course, itshould be recognized that all isoforms and mutants of BoNT proteaserecognition and cleavage sequences are also deemed suitable for use inconjunction with the teachings presented herein so long as such formsand mutants are also cleavable by one or more BoNT proteases. Forexample, suitable protease recognition and cleavage sequences includethose from VAMP (Synaptobrevin) 1, 2, 3, 4, 5, 6, 7, or 8, and exemplarysequences are listed below where the recognition and cleavage domain isin regular type font, the transmembrane domain is in cursive type font,and where the actual cleavage positions for the respective BoNTproteases are underlined (QK: BoNT/F; KL: BoNT/D; QF: BoNT/B and TeTN;AA: BoNT/G):

Rat Vamp2 Protein sequence (SEQ ID NO: 7): SEQ ID NO: 7MSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILG VICAIILIIIIVYFSTMouse Vamp2 Protein sequence (SEQ ID NO: 8): (SEQ ID NO: 8)MSATAATVPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILG VICAIILIIIIVYFSTHuman Vamp2 Protein sequence (SEQ ID NO: 9): (SEQ ID NO: 9)MSATAATAPPAAPAGEGGPPAPPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDQKLSELDDRADALQAGASQFETSAAKLKRKYWWKNLKMMIILG VICAIILIIIIVYFST

Of course, it should be noted that the above sequences merely serve asexamples for the sequences from which the transmembrane domain and theBoNT protease recognition and cleavage sequences can be obtained from.Thus, it is also noted that numerous alternative sequences other thansynaptobrevin are also contemplated particularly if they can be cleavedby a naturally occurring or a synthetic or designer BoNT, includingSNAP-25 and mutant forms thereof.

It should further be appreciated that one or more of the transmembranedomain, the first and second fluorescent proteins, and the BoNT proteaserecognition and cleavage domain may be truncated while retaining therespective function (i.e., transmembrane anchor, fluorescence, BoNTprotease recognition and cleavage). Moreover, it should be appreciatedthat one or more amino acids in the above elements may be deleted orreplaced by one or more other amino acids, typically in a conservedfashion.

Moreover, it is especially contemplated that the additional amino acidsmay be added as spacers between one or more of the transmembrane domain,the first and second fluorescent proteins, and the BoNT proteaserecognition and cleavage domain. Such spacers may be included to providefurther steric flexibility, increase distance between the elements, etc.Typically, suitable spacers will have a length of between 1-100 aminoacids, more typically between 2-50 amino acids, and most typicallybetween 3-12 amino acids. Where the recombinant protein is used for FRETassays, shorter spacers are generally preferred. Still further, it isnoted that additional domains may be provided to impart further desiredfunctions. For example, suitable additional domains will includeaffinity tags for ease of isolation or antibody-based labeling, celltrafficking to direct the recombinant protein into a desiredcompartment, etc.

With respect to the transfected cells expressing the hybrid protein itis generally preferred that the cell is stably transfected.Nevertheless, transient transfection is also contemplated. There arenumerous promoter structures known in the art, and all of those aregenerally deemed suitable for use herein. However, it is especiallypreferred that the expression is inducible from the promoter. In furthercontemplated aspects, expression may also be constitutively. FIG. 3Adepicts an exemplary vector map for an expression construct of a hybridprotein having a structure of A-B-C-D, and FIG. 3B depicts an exemplaryvector map for expression of two hybrid proteins having a structure ofA-C-B and A-C-D, respectively.

Particularly preferred cells for transfection include neuronal cells(e.g., astrocytes, dendrocytes, glia cells, etc.) and stem cells (e.g.,adult pluripotent, or adult germ line layer, or adult progenitor).However, numerous other non-neuronal cells, including human, rodent,insect cells, and even yeast and bacterial cells are also contemplatedherein.

Consequently, the inventors contemplate a cell-based method of measuringprotease activity of a BoNT protease in which in one step a transfectedcell is provided that produces (I) a hybrid protein having a structureof A-B-C-D or (II) two hybrid proteins having a structure of A-C-B andA-C-D, respectively, wherein A is a transmembrane domain, B is a firstfluorescent protein, C is a BoNT recognition and cleavage sequence, andD is a second fluorescent protein. In exemplary aspects of the inventivesubject matter, the hybrid protein having a structure of A-B-C-D has asequence according to SEQ ID NO:2, which is preferably encoded by anucleic acid having sequence according to SEQ ID NO:1. Where the hybridproteins have a structure of A-C-B and A-C-D, the protein sequences willpreferably be as shown in SEQ ID NO:4 and SEQ ID NO:6, which arepreferably encoded by a nucleic acid having sequence according to SEQ IDNO:3 and SEQ ID NO:5, respectively. Of course, and as already notedearlier, all mutant forms of the above sequences are also expresslycontemplated herein, so long as such mutant forms retain the respectivefunctions as noted above. In another step, the transfected cell iscontacted with a BoNT protease under conditions to allow the cell totake up the BoNT protease, and in yet another step, fluorescence ismeasured from at least one of the first and second fluorescent proteinsin the transfected cell.

Depending on the particular requirements and conditions, contemplatedcell based assays may be performed as depicted in FIG. 2A in which thehybrid protein is a single polypeptide chain having an N-terminaltransmembrane domain, followed by a CFP, which is in turn followed by aBoNT protease recognition and cleavage sequence, which is in turnfollowed by a (preferably terminal) YFP. Expression of the hybridprotein and subsequent translocation of the hybrid protein to themembrane of an intracellular vesicle will result in the presentation ofthe hybrid protein on the outside of the vesicle. The protease activityof BoNT/B will then intracellularly cleave the cleavage sequence, thusreleasing the YFP from the hybrid protein. Consequently, quenching isreduced and fluorescence of the YFP is detectable in diffused form fromthe cell.

Alternatively, as shown in FIG. 2B, two separate hybrid proteins areformed in the cell, each having an N-terminal transmembrane domain,followed by a BoNT protease recognition and cleavage sequence, which isin turn followed by a (preferably terminal) YFP and CFP, respectively.Expression of the hybrid proteins and subsequent translocation of thehybrid proteins to the membrane of an intracellular vesicle will resultin the presentation of the hybrid proteins on the outside of thevesicle. The protease activity of BoNT/B will then intracellularlycleave the cleavage sequences, thus releasing YFP and CFP from thehybrid protein. Consequently, quenching is reduced and fluorescence ofthe YFP and CFP is detectable in diffused form from the cell.Remarkably, the respective hybrid proteins co-locate on the vesicularmembrane in such a manner as to allow for FRET. Exemplary results forsuch assays are depicted in the calculated fluorescence microphotographsof FIG. 4A and the corresponding bar graph representations of FIG. 4B.As can be readily taken from these figures, the FRET assay performedwell in the intermolecular FRET assay and less satisfactorily in theintramolecular FRET assay. However, it is expected that routineexperimentation will also provide satisfactory intramolecular FRET assayresults.

In other embodiments, two separate hybrid proteins are formed in thecell, each having an N-terminal transmembrane domain. One of the hybridproteins includes a fluorophore (for example, a peptide fluorophorederived from Green Fluorescent Protein) and a BoNT protease recognitionsequence and cleavage sequence that intervenes between and is joined toboth the transmembrane domain and the fluorophore. The second hybridprotein includes a second, different fluorophore (for example, adifferent peptide fluorophore derived from Green Fluorescent Protein)and a second, distinct non-cleavable intervening peptide sequence thatdoes not include a BoNT cleavage sequence and is joined to both thetransmembrane domain and the fluorophore. In some embodiments the secondintervening peptide sequence can include a BoNT protease recognitionsequence or a portion of a BoNT substrate protein, but does not includea BoNT cleavage sequence. In such a second hybrid protein the BoNTcleavage sequence can be partially or completely excised, modified bysubstitution with non-native amino acids, or be modified bypost-translational modification (for example, treatment with reagentsreactive with amino acid side chains). Peptide sequences associated withrecognition by BoNTs and the sequences associated with cleavage by BoNTscan be found in the literature, for example in Sikorra et al.,“Substrate Recognition Mechanism of VAMP/Synaptobrevin-cleavingClostridial Neurotoxins” J. Biol. Chem. 283(30):21145-21152 (2008).

In such an embodiment the two hybrid proteins can associate and form allor part of a reporting construct complex. On exposure to a BoNT havingspecificity for the cleavage site sequence (for example, exposure of asynaptobrevin-based reporting construct complex to BoNT/B), only thefluorophore associated with the cleavage site-containing interveningsequence is released, whereas the fluorophore associated with theintervening sequence that does not include such a cleavage site isretained at the membrane. In preferred embodiments, the fluorophoreassociated with the cleavage site-containing intervening sequence isselected to be degradable by components of the cytosol, and release by aBoNT results in degradation of the released fluorophore relative tofluorophore associated with the membrane. In some embodiments, such areleasable fluorophore is selected to be more rapidly degraded (forexample 1.5, 3, 10, 30, 100, or more than 100 times faster) in thecytosol than the fluorophore associated with the non-cleavableintervening sequence if found in the cytosol. For example, YFP can beassociated with the cleavage site—containing intervening sequence andCFP can be associated with the intervening sequence that lacks a BoNTsusceptible cleavage site. In some embodiments the fluorophores can beselected, oriented, and/or spaced such that meaningful (i.e. >5%)Foerster resonance energy transfer occurs between donor and acceptorfluorophore. In other embodiments, the fluorophores can be selected,oriented, and/or spaced such that no meaningful (i.e. less than or equalto 5%) Foerster resonance energy transfer occurs between thefluorophores.

In such embodiments, the fluorophore associated with the interveningsequence that lacks a BoNT cleavage sequence remains associated with amembrane following exposure to a BoNT. The emission from such afluorophore can be utilized to normalize the emission observed from thefluorophore that is associated with the intervening sequence thatincludes a BoNT cleavage site, for example by calculating a ratio. Suchnormalization can be used to reduce assay variation resulting fromdifferences in cell density, size, and/or distribution between differentwells of test plate in a cell-based assay for BoNT activity.

FIGS. 5A and 5B depict an embodiment of the inventive concept in whichtwo hybrid proteins, one of which is not cleaved by a BoNT, areutilized. FIG. 5A shows a membrane 510 (for example, a vesicle membrane)that includes a reporting construct complex 520 prior to theintroduction of or in the absence of a BoNT. The reporting constructcomplex includes at least two peptides. One peptide includes a firstfluorophore 550 that is coupled to a transmembrane portion 565 by anintervening peptide 560. The intervening peptide 560 includes BoNTrecognition and BoNT cleavage sequences, and hence is susceptible tocleavage by the proteolytic activity of a BoNT having specificity forthose recognition and cleavage sequences. The other peptide includes asecond fluorophore 530 that is coupled to a transmembrane portion 545 byan intervening peptide 540. The intervening peptide 540 is not cleavableby the BoNT that is capable of cleaving intervening peptide 560. In someembodiments the intervening peptide 540 is an analog of interveningpeptide 560 (i.e. having 50%, 60%, 70%, 80%, 90%, 95%, or greater than95% sequence identity) that does not include the BoNT cleavage site. Forexample, the intervening peptide 560 can include a synaptobrevinsequence than includes BoNT/B recognition and BoNT/B cleavage sequences,whereas intervening peptide 540 can include a synaptobrevin sequencethat retains BoNT/B recognition sequences and does not include theBoNT/B cleavage sequence. The fluorophores 530 and 550 aredistinguishable from one another (for example, by having differentexcitation/emission spectra), and can be selected and positioned (i.e.via spacing and/or orientation) to form a FRET pair, for example byselecting fluorophore 530 to have an emission spectrum that overlaps theexcitation spectrum of fluorophore 550. In other embodiments thefluorophores can be selected and/or positioned such that significantFRET (i.e. >5%) does not occur.

FIG. 5B depicts the result of exposure of the reporting constructcomplex of FIG. 5A to a BoNT capable of cleaving the intervening peptide560. As shown, such cleavage results in the cleavage of the interveningpeptide into two fragments, 560A and 560B. Fragment 560B remains withthe transmembrane sequence 565 while fragment 560 remains with theassociated fluorophore 550, which is released into the cytoplasm. Sinceintervening peptide 540 is not cleaved, fluorophore 530 remains attachedto the membrane following exposure to the BoNT. Release of fluorophore550 can (in the case of reporting construct complexes exhibiting FRET)result in loss of FRET that is detectable by loss of emissions from thefluorophore. In addition, release into the cytosol can result indegradation of fluorophore 550, which can be detected by loss ofemission from the fluorophore. Fluorophore 530, however, is not subjectto cytosolic degradation, and as a result emission continues followingBoNT treatment. In some embodiments an emission measurement from thefluorophore retained on the membrane following BoNT exposure is used tocorrect for variations in cell density, size, and/or distributionbetween wells of a test plate. This can be accomplished, for example, bycalculating a ratio between the fluorescence emission measured from thefluorophore released by BoNT treatment and the fluorescence emissionmeasured from the fluorophore retained following BoNT treatment.

EXAMPLES Cloning of Intramolecular Construct

The intramolecular FRET construct, pMD0031 (FIG. 3A), was constructed inpEGFP-C1 (Clontech, Mountain View, Calif.). Three DNA fragments—anN-terminal fragment of rat Vamp2 from the start to amino acid 92, fulllength YFP without a stop codon, and a C-terminal fragment of rat Vamp2from amino acid 93 to the stop—were amplified by polymerase chainreaction (PCR). An EcoRI restriction site was engineered onto the 5′ endof the N-terminal Vamp2 fragment and a SerGlyGly (TCGGGAGGC) linker andthe first 12 nucleotides of the YFP were engineered onto the 3′ end. TheYFP fragment had the last 13 nucleotides of the N-terminal Vamp2fragment and the same SerGlyGly linker as the N-terminal Vamp2 fragmentengineered onto the 5′ end and a second SerGlyGly (AGCGGCGGT) linker andthe first 9 nucleotides of the C-terminal Vamp2 fragment engineered ontothe 3′ end. The C-terminal Vamp2 fragment had the last 12 nucleotides ofYFP without a stop and the same SerGlyGly linker as the YFP fragmentengineered onto the 5′ end and a BamHI restriction site engineered ontothe 3′ end.

These three fragments were then combined using splice overlap extension(SOE) PCR to create a single fragment consisting of an EcoRI restrictionsite, the N-terminal fragment of rat Vamp2 (amino acids 1-92), aSerGlyGly linker, YFP without a stop, a second SerGlyGly linker, theC-terminal fragment of rat Vamp2 (amino acids 93-stop), and an BamHIrestriction site. This fragment and pECFP-C1 were then digested withEcoRI and BamHI, ligated together, and transformed into DH5αE. coli. Thefinal construct insert was then fully sequenced.

Cloning of Intermolecular Construct

The intermolecular FRET construct, pMD0034 (FIG. 3B), was constructed inpBudCE4.1 (Invitrogen, Carlsbad, Calif.). The YFP rat Vamp2 fusion wasgenerated by amplifying two fragments by PCR. The first fragment was YFPwithout a stop with an engineered HindIII restriction site on the 5′ endand a SerGlyGly linker (AGTGGAGGC) and the first 9 nucleotides of ratVamp2 engineered on the 3′ end. The second fragment was full length ratVamp2 with the last 9 nucleotides of YFP and the same SerGlyGly linkerengineered onto the 5′ end and an XbaI restriction site engineered ontothe 3′ end. These two fragments were then combined using SOE PCR tocreate a YFP, SerGlyGly linker, full length Vamp2 fragment. The fragmentand pBudCE4.1 was then digested with HindIII and XbaI, ligated together,and transformed into DH5 αE. coli. The CFP rat Vamp2 fusion was createdsimilarly but contained a CFP without a stop, a NotI restriction site onthe 5′ end, and a KpnI site on the 3′ end. The final construct was thenfully sequenced.

Cell Culture and FRET Assay

Analysis of FRET efficiency, YFP/CFP fluorescence ratios, and BoNT/Bsensitivities of the BoNT/B reporters was performed in cells in vitro.More specifically, Neuro2A cells were grown in a 96-well plate to 70%confluency (2000 cells/well) and transiently transfected usingLipofectamine 2000 (Invitrogen), with the intra-or intermolecular BoNT/Breporters. After 24 h, cells were incubated in the presence or absenceof 25 nM BoNT/B at 37° C. for 72 h in 100 μl of phenol red-free MEMmedium.

Semi-automated FRET or total YFP and CFP fluorescence measurements wereperformed using a Nikon TE2000-U fluorescent microscope with 200×magnification and Nikon NIS Elements 3.4 software. For FRETmeasurements, coefficients −A and −B (acceptor and donor) werecalculated at 0.03 and 0.73 respectively, using a specific bleed-throughmethod. FIG. 4A depicts randomly selected fields pseudo-colored for FRETefficiency or the YFP/CFP fluorescence ratio. YFP/CFP ratios werecalculated from emissions collected upon direct excitement of eachfluorophore. As can be seen from the graphic representation in FIG. 4B,the intermolecular BoNT/B reporter approach was significantly moresensitive for detection of BoNT/B in living cells. 30 randomly selectedcells per condition were analyzed for FRET efficiency (FIG. 4A, leftpanels) or YFP/CFP fluorescence ratios (FIG. 4A, right panels) in thepresence or absence of 25 nM BoNT/B. Indeed, such results were entirelyunexpected as effective intermolecular FRET not only required balancedexpression of the two fluorescent proteins, but also co-location of therecombinant proteins in corresponding quantities. The average signalfrom the 30 cells from 5 microscopic fields on 3 different wells isshown. Cells exhibiting over-saturated fluorescence were excluded.

Thus, specific embodiments and applications of BoNT assays have beendisclosed. It should be apparent, however, to those skilled in the artthat many more modifications besides those already described arepossible without departing from the inventive concepts herein. Theinventive subject matter, therefore, is not to be restricted except inthe spirit of the appended claims.

What is claimed is:
 1. A transfected cell comprising: a cytosol; anucleic acid comprising a sequence that encodes a first hybrid proteinhaving a structure of A-C-B and a second hybrid protein having astructure of A-C′-D; wherein A is a transmembrane protein domain ofsynaptobrevin target to an intracellular vesicle membrane and that isnot cleavable by a Botulinum neurotoxin protease, B is a firstfluorescent protein, C is a first linking region comprising a Botulinumneurotoxin protease recognition sequence and a Botulinum neurotoxinprotease cleavage sequence, C′ is second linking region comprising ananalog of C that includes the Botulinum neurotoxin protease recognitionsequence but not the Botulinum neurotoxin protease cleavage sequence, Bis a first fluorescent protein and D is a second fluorescent protein,wherein the first fluorescent protein is selected to be degradable by acomponent of the cytosol, selected to form a FRET pair with the firstfluorescent protein, and wherein the first fluorescent protein and thesecond fluorescent protein are selected, oriented, or spaced such thatless than or equal to 5% FRET occurs between the first fluorescentprotein and the second fluorescent protein when the first hybrid proteinand the second hybrid protein are collocated with a vesicle of thetransfected cell.
 2. The transfected cell of claim 1, wherein the firsthybrid protein further comprises a first spacer amino acid sequenceinterposed between at least one of the transmembrane protein domain andthe first linking region and the first linking region and the firstfluorescent protein.
 3. The transfected cell of claim 2, wherein thefirst spacer amino acid sequence is between 1 and 100 amino acids inlength.
 4. The transfected cell of claim 1, wherein the second hybridprotein further comprises a second spacer amino acid sequence interposedbetween at least one of the transmembrane protein domain and the secondlinking region and the second linking region and the second fluorescentprotein.
 5. The transfected cell of claim 4, wherein the second spaceramino acid sequence is between 1 and 100 amino acids in length.
 6. Thetransfected cell of claim 1 wherein the transfected cell is stablytransfected with the nucleic acid.
 7. The transfected cell of claim 1wherein the transfected cell is a cell selected from the groupconsisting of a neuronal cell, a neuroendocrine tumor cell, a hybridcell, and a stem cell.
 8. The transfected cell of claim 1, wherein C andC′ are derived from synaptobrevin.
 9. A cell-based method of measuringprotease activity of a BoNT protease, comprising: providing thetransfected cell of claim 1; contacting the transfected cell with a BoNTprotease under conditions to take up the BoNT protease by thetransfected cell; and measuring a first fluorescence emission from saidtransfected cell, thereby measuring protease activity of said BoNTprotease.
 10. The cell-based method of claim 9, wherein the firstfluorescence emission is provided by the first fluorescent protein. 11.The cell-based method of claim 9, further comprising a step of measuringa second fluorescence emission from the transfected cell, wherein thesecond fluorescence emission is provided by the second fluorescentprotein.
 12. The cell-based method of claim 11, further comprising astep of normalizing the first fluorescence emission using the secondfluorescence emission.
 13. The method of claim 9, wherein thetransfected cell is a cell selected from the group consisting of aneuronal cell, a neuroendocrine tumor cell, a hybrid cell, and a stemcell.
 14. The method of claim 9, further comprising a step of contactingthe transfected cell with a putative BoNT inhibitor prior to contactingthe transfected cell with the BoNT protease.
 15. A recombinant nucleicacid comprising: a sequence that encodes a first hybrid protein having astructure of A-C-B and a second hybrid protein having a structure ofA-C′-D; wherein A is a transmembrane protein domain of synaptobrevintargeted to an intracellular vesicle membrane and that is not cleavableby a Botulinum neurotoxin protease, B is a first fluorescent protein, Cis a first linking region comprising a Botulinum neurotoxin proteaserecognition sequence and a Botulinum neurotoxin protease cleavagesequence, C′ is second linking region comprising an analog of C thatincludes the Botulinum neurotoxin protease recognition sequence but notthe Botulinum neurotoxin protease cleavage sequence, B is a firstfluorescent protein and D is a second fluorescent protein, wherein thefirst fluorescent protein is selected to be degradable by a component ofthe cytosol, selected to form a FRET pair with the first fluorescentprotein, and wherein the first fluorescent protein and the secondfluorescent protein are selected, oriented, or spaced such that lessthan or equal to 5% FRET occurs between the first fluorescent proteinand the second fluorescent protein when the first hybrid protein and thesecond hybrid protein are collocated with a vesicle.
 16. The recombinantnucleic acid of claim 15 wherein C comprises at least one of the groupconsisting of a Botulinum neurotoxin/B protease recognition and proteasecleavage sequence, a Botulinum neurotoxin/G protease recognition andprotease cleavage sequence, a Botulinum neurotoxin/D proteaserecognition and protease cleavage sequence, and a Botulinum neurotoxin/Fprotease recognition and protease cleavage sequence, and wherein C′comprises at least one of the group consisting of a Botulinumneurotoxin/B protease recognition sequence absent the correspondingprotease cleavage sequence, a Botulinum neurotoxin/G proteaserecognition sequence absent the corresponding protease cleavagesequence, a Botulinum neurotoxin/D protease recognition sequence absentthe corresponding protease cleavage sequence, and a Botulinumneurotoxin/F protease recognition sequence absent the correspondingprotease cleavage sequence.